view tools/myTools/3_insilico_attrs.xml @ 1:7e5c71b2e71f draft default tip

Uploaded

<tool id="netisce3" name="Netisce Step 3" version="0.1.0" python_template_version="3.5">
<description>Estimates the attractors for randomly generated initial states using signal flow analysis</description>

    <requirements>
        <requirement type="package" version="1.1.5">pandas</requirement>
        <requirement type="package" version="1.19.5">numpy</requirement>
        <requirement type="package" version="3.5.0">os</requirement>
        <requirement type="package" version="1.11.0">networkx</requirement>
        <requirement type="package" version="3.5.0">random</requirement>
        <requirement type="package" version="3.5.0">sys</requirement>
        <requirement type="package" version="3.5.0">csv</requirement>
        <requirement type="package" version="3.1.14">sfa</requirement>
        <requirement type="package" version="1.0.3">statistics</requirement>
    </requirements>

    <command>python3 '$__tool_directory__/bin/SFA_insilico.py' '$network' '$expression_data' '$samples' '$num_states'</command>

    <inputs>
        <param name="network" type="data" format="sif" label="Network"/>
        <param name="expression_data" type="data" format="csv" label="Expression Data"/>
        <param name="samples" type="data" format="txt" label="Name of Experimental Samples"/>
        <param name="num_states" type="integer" value="10000" label="Num of Insilico Attractors to Generate"/>
    </inputs>

    <outputs>
        <data name="output" format="tabular" from_work_dir="attrs_insilico.tsv" label="Insilico Attractors"/>
    </outputs>

    <tests>
        <test>
            <param name="network" value="network.sif" />
            <param name="expression_data" value="expressions.csv" />
            <param name="num_states" value="10000"/>
            <param name="samples" value="samples.txt" />
            <output name="output" file="attrs_insilico.tsv" ftype="tsv" />
        </test>
    </tests>

    <help>
    This tool estimates the attractors for randomly generated initial states using signal flow analysis.
    Required Inputs:
    1. network in sif format (activating edges as "activates", inhibitory edges as "inhibits")
    2. normalized expression values for data sample
    3. experimental sample names of interest
    4. number of insilico Attractors to generate (default = 10,000)
    </help>

    <citations>
        <citation type="doi">10.1038/s41598-019-50790-0</citation>
    </citations>

</tool>